problem with rasterToPolygons x worldclim

On Thu, 7 Apr 2016 at 00:22 Michael Sumner <mdsumner at gmail.com> wrote:

On Wed, 6 Apr 2016 at 23:45 Karla Shikev <karlashikev at gmail.com> wrote:

Hi Michael,

Thanks for the tips. I tried the help for rasterToPolygons, but none of
the options (e.g. dissolve=TRUE) made any difference. I tried gPolygonize
and it worked, except for (as you predicted), if the edges meet the raster
extents - but that definitely was an advance!

I see the issue, the fun argument to rasterToPolygons is masking out
values from that interval, but it's not setting them all to the same value
- so you still get individual pixel polygons unless you mask on presence in
the interval or not (as a binary):

library(raster)

r<-getData('worldclim', var='bio', res=10)$bio1

e <- extent(-140,-100, 50, 60)

xx <- crop(r,e)
## mask out pixel values first
xx <- xx > 40 & xx < 60

## 576 polygons
slice1<- rasterToPolygons(xx, fun = function(x) {x == 1})
## 1 polygon
slice2 <- rasterToPolygons(xx,  fun = function(x) {x == 1}, dissolve =
TRUE)


Still it's not a very nice polygon, if I can I'll try a different way.

Cheers, Mike.

You can use tricks to fill the outer edge so you get a valid contour line
all the way around (it's not always going to work - see here for the
explanation by whuber:
http://gis.stackexchange.com/questions/61550/colouring-areas-between-vector-contours
)

Is this better? Maybe - there are lots of other ways - maybe a buffer on
this gives roughly what you need. Maybe you only need a total area so
summing pixels after filtering is better?

Would be nice to have contouring that reliably produced polygons, but it's
a tricky problem. Other kinds of shape-finding might be better, with
alphahull on the pixel points perhaps, but you quickly get into "geometry
fudger" territory here rather than objective measures.

HTH

I really appreciate your help and if you just point the way I can try to
go after what needs to be done, but right now I?m stumped.

best, Karla.

On Mon, Apr 4, 2016 at 5:38 PM, Michael Sumner <mdsumner at gmail.com>
wrote:

Read the help for rasterToPolygons, alternatively try chaining
rasterToContour and rgeos::gPolygonize.

The latter may need coaxing if your edges meet the raster extents.

Cheers, Mike

On Tue, 5 Apr 2016, 05:32 Karla Shikev <karlashikev at gmail.com> wrote:

Dear all,

Here's an issue that is related to the previous one. In the commands
below
I'm trying to make a polygon for all the regions within a range of mean
annual temps. However, rasterToPolygons will draw a square around each
value in the original raster, rather than providing me the actual
polygon,
given that resolution. Any hints? Again, any help will be greatly
appreciated.

Karla

_____

library(raster)

r<-getData('worldclim', var='bio', res=10)$bio1

e <- extent(-140,-100, 50, 60)

xx<-crop(r,e)

slice1<-rasterToPolygons(xx, fun = function(x) {x > 40 & x < 60})

plot(slice1)

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--
Dr. Michael Sumner
Software and Database Engineer
Australian Antarctic Division
203 Channel Highway
Kingston Tasmania 7050 Australia

--

Dr. Michael Sumner
Software and Database Engineer
Australian Antarctic Division
203 Channel Highway
Kingston Tasmania 7050 Australia

--

Dr. Michael Sumner
Software and Database Engineer
Australian Antarctic Division
203 Channel Highway
Kingston Tasmania 7050 Australia

--